Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  TRANSCRIPTIONAL REPRESSOR COPG
 
Authors :  F. X. Gomis-Rueth, M. Sola, P. Acebo, A. Parraga, A. Guasch, R. Eritja, A. Gonzalez, M. Espinosa, G. Del Solar, M. Coll
Date :  15 Nov 99  (Deposition) - 19 Nov 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Keywords :  Transcriptional Repressor, Dna-Binding Protein, Plasmid, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. X. Gomis-Ruth, M. Sola, P. Acebo, A. Parraga, A. Guasch, R. Eritja, A. Gonzalez, M. Espinosa, G. Del Solar, M. Coll
The Structure Of Plasmid-Encoded Transcriptional Repressor Copg Unliganded And Bound To Its Operator.
Embo J. V. 17 7404 1998
PubMed-ID: 9857196  |  Reference-DOI: 10.1093/EMBOJ/17.24.7404
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REPRESSOR COPG
    Cellular Location: PLASMID PMV158
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMV158
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DNA-BINDING PROTEIN
    Organism Scientific: STREPTOCOCCUS AGALACTIAE
    Organism Taxid: 1311
    Strain: PLS1
    Synonym: REPA PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (2x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS B:28 , ARG C:22 , HOH C:60BINDING SITE FOR RESIDUE CL B 46
2AC2SOFTWAREARG B:22 , LYS C:28BINDING SITE FOR RESIDUE CL C 46
3AC3SOFTWARESER A:29 , HOH B:64BINDING SITE FOR RESIDUE CL A 46

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CPG)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Met C:1 -Lys C:2

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CPG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2CPG)

(-) Exons   (0, 0)

(no "Exon" information available for 2CPG)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:43
 aligned with COPG_STRAG | P13920 from UniProtKB/Swiss-Prot  Length:45

    Alignment length:43
                                    10        20        30        40   
            COPG_STRAG    1 MKKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKGQ 43
               SCOP domains d2cpga_ A: Transcriptional repressor CopG   SCOP domains
               CATH domains 2cpgA00 A:1-43 Met repressor-like           CATH domains
               Pfam domains ------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeehhhhhhhhhhhhhh...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------- PROSITE
                 Transcript ------------------------------------------- Transcript
                  2cpg A  1 MKKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKGQ 43
                                    10        20        30        40   


Chain B from PDB  Type:PROTEIN  Length:45
 aligned with COPG_STRAG | P13920 from UniProtKB/Swiss-Prot  Length:45

    Alignment length:45
                                    10        20        30        40     
            COPG_STRAG    1 MKKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKGQEK 45
               SCOP domains d2cpgb_ B: Transcriptional repressor CopG     SCOP domains
               CATH domains 2cpgB00 B:1-45 Met repressor-like             CATH domains
               Pfam domains --------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------- PROSITE
                 Transcript --------------------------------------------- Transcript
                  2cpg B  1 MKKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKGQER 45
                                    10        20        30        40     


Chain C from PDB  Type:PROTEIN  Length:42
 aligned with COPG_STRAG | P13920 from UniProtKB/Swiss-Prot  Length:45

    Alignment length:42
                                    10        20        30        40  
            COPG_STRAG    1 MKKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKG 42
               SCOP domains d2cpgc_ C: Transcriptional repressor CopG  SCOP domains
               CATH domains 2cpgC00 C:1-42 Met repressor-like          CATH domains
               Pfam domains ------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhh...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------ PROSITE
                 Transcript ------------------------------------------ Transcript
                  2cpg C  1 MKKRLTITLSESVLENLEKMAREMGLSKSAMISVALENYKKG 42
                                    10        20        30        40
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CPG)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (COPG_STRAG | P13920)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0006276    plasmid maintenance    The maintenance of the integrity of extrachromosomal plasmid DNA; includes processes that ensure plasmids are retained in the daughter cells after cell division.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Met C:1 - Lys C:2   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2cpg
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  COPG_STRAG | P13920
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  COPG_STRAG | P13920
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        COPG_STRAG | P13920: 1b01 1ea4

(-) Related Entries Specified in the PDB File

1b01 REPA PROTEIN COMPLEXED WITH DNA